I have noticed an issue when I am running 'findchrompeaks Merger' XCMS step on my dataset.
I enter the good inputs (*.raw.xset.RData) for this step that I had already performed several times, but this time it goes through error.
I think that this errors occurs because I have permanently deleted the mzml files a few minutes before - to free up some space on disk. Is that right? So may I just re-upload the mzml files and go for merger step directly or do I have to run again findchrompeaks step?
Indeed, the error occurs because the original mzML file is missing. In fact, the XCMS workflow needs the original data at several steps, meaning you need to keep your files until you reach the final XCMS step.
In case you do not have access to the original files anymore for any reason, you need to ensure a new access to the corresponding data. Once you have re-uploaded the data, there is an option in each XCMS module that allows you to re-define where the corresponding data are:
